1. most important.
hydrogen bar position "1" is always position "1" in ardour.
that mean, all songs starts here. its impossible to start a hydrogen song on position 1 if your song in ardour begins e.g on bar 21. this never work in moment.

2. never change song length in hydrogen if transport is running. hydrogen have to recalculate a lot of internal positions variables.

3. complexer setups with different pattern lengths needs a adapted timeline in ardour. otherwise you get out of sync. ardours default settings here are 120bpm with 4/4 resolution. you have to make this clear if you work with different beat lengths and tempo change.